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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttctttattctatacatatttctatctatccacatccactgttgaaatgcatattcaaaagaagagctggtgtgcctagccattctcaggctt...

Basic information

species Zea mays
transcript GRMZM2G165926_T02
intron # 10
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37380959|gb|CF627330.1|CF627330
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|18162870|gb|BM332709.1|BM332709
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|5525732|gb|AI861625.1|AI861625
EST:     GACAAAACAGAAGACGAGAAGAACTGATG-AGCCATGTTCACGCTTC-AT                         GCGTACAAAGAAAT
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAAT
EST: gi|71419000|gb|DR804613.1|DR804613
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|37398277|gb|CF636450.1|CF636450
EST:     GACAAAACAGAAGACGATAAGAACTGATAT-GCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60337128|gb|DN204101.1|DN204101
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60353359|gb|DN220332.1|DN220332
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|211072582|gb|FL217263.1|FL217263
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60347266|gb|DN214239.1|DN214239
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|37383110|gb|CF628537.1|CF628537
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|31664308|gb|CD573033.1|CD573033
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTC-CGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCC-TTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60349443|gb|DN216416.1|DN216416
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60346958|gb|DN213931.1|DN213931
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|33097806|gb|CF057766.1|CF057766
EST:     GACAAAACAGAAGACGAGAAGAACTGATGTAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|18174967|gb|BM350355.1|BM350355
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGCTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|211072583|gb|FL217264.1|FL217264
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60357544|gb|DN224517.1|DN224517
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTTTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|211442872|gb|FL468446.1|FL468446
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60354620|gb|DN221593.1|DN221593
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|5847367|gb|AW000446.1|AW000446
EST:     GACAAAACAGAAGACGAGAAGAACTGATGTAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|5706125|gb|AI941901.1|AI941901
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|44901350|gb|CK827895.1|CK827895
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTGAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|60399456|gb|DN232268.1|DN232268
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
EST: gi|37383796|gb|CF628931.1|CF628931
EST:     GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT                         GCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG
genomic: GACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 187

CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTGGTCGTGGAGTTTGTTTATCCTCATATAACGGTGCTTTGATTATAACTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 156

CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTGGTCGTGGAGTTTGTTTATCCTCATATAACGGTGCTTTGATTATAACTTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTGGTCGTGGAGTTTGTTTATCCTCATATAACGGTGCTTTGATTATAACTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttc ... gacttcgcagGCGTACAAAGAAATTAAAGACCGGTCTCCATTGACTGCGTTTACTCTCTTGGTCGTGGAGTTTGTTTATCCTCATATAACGGTGCTTTGATTATAACTTA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCATgtaagcgttctttattctatacatatttctatctatccacatccactgttgaaatgcatattcaaaagaagagctggtgtgcctagccattctcaggctt

- - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaagaa